Metabonomic techniques have been used to discover subtle differences in the small-molecule profiles of chicken eggs, which could help to combat fraud within the egg industry. High-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (HPLC-Q-ToF-MS) was used to obtain profiles of the small molecules present in the yolks of chicken eggs stored for different lengths of time. Statistical analysis, including the use of XCMS Online and further exploratory statistics, was able to uncover differences in the abundances of several of the small molecules found in these egg yolks. One of these small molecules was identified through the use of METLIN and MS/MS analysis as choline. A targeted study was then carried out over a longer storage period, using the same instrumentation and analytical techniques, in order to observe how the concentration of choline in egg yolk changes over a longer period of time.